Saturday, January 18, 2014

The Short Attention Span Segement: #10

So it's Saturday, and instead  pursuing things I like to do on a weekend such as thesis writing,  I'm at the lab doing experiments that need to be done, all on the back of a rather intoxicating night last night. Lucky the head isn't hurting - whiskey and I tend to get along and I didn't have too many....

While I wait for an A-tailing reaction to occur, here's the return of the Short Attention Span Segment otherwise known as SASS, otherwise known as a small list of cool stuff I found this week and would like to share: 

1. What happens when you make an open-production company bringing together thousands of artists of all types from around the world? Music, drawings, text, film, painting, animation, all made collaboratively, that's what! The results are just awesome. I love this concept and it's now a show! And it's the headed up by the always adorable Joseph Gordon Levitt:  HitRecord Variety Show

2. I love pirates. everyone should love pirates. They say "ARGH" and drink rum and have crazy adventures. A bit like me I guess, except replace the rum with whiskey. I also like recycling, upcycling, reusing, and creative uses for old things. This combines both: A life-size pirate ship made entirely out of reused cardboard

3. Ever wondered just how the Walter White made meth on "Breaking Bad"? Some researchers have figured out a possible way he did it without then need for cold and flu tablets:  Walter White's recipe analysed

4. Art meets Science. The staple of the microbiologist, the Petri dish, turned into a daily art project and the results are stunning: The Daily Dish

5. And finally, the man who was a witty word wizard, the ever-missed Christopher Hitchens on where to look if you need to be awe inspired:  Hitch on Awe

And look at that, a few minutes to spare before I have to get back to the lab!

Tuesday, January 14, 2014

So what is it you do as a 'scientist' anyway?

Surprisingly, explaining the evolution of my fairly infantile career and even my current job can sometimes be a bit of a challenge. I mean how does someone go from forensic science to neurogenetics? Why do you get all excited? And are lab coats really comfortable (A: yes, yes, they are.)

I think if I have to define my job, I'd probably say I'm a molecular biologist who has a big focus on methods to analyse genetic data. Some may think this relates to engineering super-viruses a la 28 days later, or building Frankenstein. Really, it's a tad less cinematic and involves working on things that are mostly invisible,  appearing as clear liquids that are generally in really small tubes!

Over on everyone's favourite social network site, my current job title is "voodoo HiSeq operator". A bit of a joke, yes, as there's no actual rituals involving snakes and Haitian zombies in my workplace.  But sometimes, science can feel more like art and magic.  Mastering molecular biology sometimes does involve a little magic, hence the job title. But jokes aside:

What's a HiSeq?

And what do you all do day that involves it (plus the occasional bit of voodoo)?

Simply, a HiSeq2000 is a large white box:

Doesn't look like much, and most of it is actually fridge space.

But it's what this seemingly inert box is capable of that is mind blowing.

A decade ago, it took 10 years to sequence a single human genome. Clearly to study the complex world that was unfolding at the genetic level, a revolution of the method to crunch genomes was needed.

And this revolution came in the form of Next Generation Sequencing (NGS). Essentially, by combining some really neat and well known molecular biology with high powered optics and imaging, instead of sequencing single, small fragments of DNA one by one with a maximum of a few hundred fragments every 8 hours or so, we were able to start sequencing millions of fragments of DNA simultaneously.

And that's where the HiSeq comes in. For around $800,000 a lab can buy one of these machines from a company called illumina and can hold the proverbial keys to the genetic kingdom in a small room.  
To give you an idea - the HiSeq has the ability to output the equivalent of 100 human genomes every 10 days. That's 100x what took 10 years a decade ago. Oh, and instead of costing over a billion dollars for a single genome, it now costs a few thousand dollars. Labs around the world have now sequenced birds, fish, plants, microbes and even extinct creatures.

So why have one of these lovely white boxes?

It's nice to generate lots of data.  Data is like crack for a scientist. We're addicted to it, it gets us high and we always want more. The better the data, the more we like it (the come down from bad data is just horrible though!).

But you should have a reason to make the investment. Generating lots of data still costs a lot of money and takes a lot of time. Having shiny new toys is great, but they should serve a purpose.

Aside from making genomic data easy and cheaper to generate, the biggest advantage of a platform such as the HiSeq is it enables the ability to study lots of individuals at an unprecedented level of detail.  

And that's where I come in. Welcome to my world:

The office aka. thinking/emailing/mulling over results space. Note: it is not always this neat.

The bench. Always this neat.

The lab. Sometimes neat, sometimes like a bomb hit it. Usually related to the amount of work going on and how many deadlines there are coming up.

I run a small genetics lab which has huge data generation capability. The focus for me is on providing genetic analysis both of DNA and RNA (the transcriptome aka. protein coding part of the genome)  using the HiSeq and similar technologies to researchers within a large neuroscience institute (and a few external projects). My research background is based in methods and technology, and I think the methods we use is my favourite thing about science. The challenge of getting from A to B,  designing experiments and generating data to answer riddles is basically my job description and what I love most - methods  underpin the answering of all scientific questions. I'm fortunate to get to work quite collaboratively, do a little of my own research and in some cases, push the boundaries and generate data that even a year ago, just wasn't possible. 

Not much bigger than a microscope slide, yet containing 1.5 billion DNA fragments ready for sequencing, this small piece of glass with 8 channels known as a flowcell. A few years ago, a single human genome took 10 years and hundreds of people. Now the same can be done in 10 days, by a single person using this technology.

Data generation in action. The coloured dots are DNA!!

I've worked on everything from sequencing large numbers of individuals to uncover rare variants associated with complex disorders to studying genetic differences in single cells. I work on samples from humans, mice, and bees. Seeing such cutting edge in technology used to unravel and answer scientific questions is just awesome, there's no doubt about it - I should note the disclaimer here: it can be a lot of work. 

I mentioned neurogenetics earlier - all this genetic data I work on generating is related to neuroscience. Think questions around how genes regulate brain development, mutations associated with motor neurone disease, the genetic basis of autism or schizophrenia and studying gene expression in learning and memory formation (just to name a few). Understanding  the nervous system is a very large and complex undertaking, with some biologists even considering it the last major frontier of biology and medical science. It is so large the U.S government is undertaking a project involving large collaborative effort to map the brain, and part of this is genetic analysis of the of the brain. 

Whether applied to neuroscience, forensic identification, evolutionary biology, medical genetics or environmental science, the technology I work with daily has revolutionised just how we study the very code for life. 

Added bonus of my job: some of the reagents I work with are pretty. 

The methods we currently use in research are also enabling the next generation in medicine and fieldwork.  Gradually this same technology is being applied to accurately diagnose the genetic basis of a disease, monitor response to medication, rapidly identify biological material and the field or confirm the identification of an individual using DNA. The era of personalised medicine and use of genetics in the field is actually on our doorstep. 

The most amazing thing for me is, the more we seem to uncover about why we differ, how we evolved, or what is happening in disease, the more complex and wonderful the genetic world seems to become. It's certainly the genomic age, and a great time to be a geneticist. We've certainly got a lot of work to do, and hopefully the technology enables us to continue pushing the boundaries and understanding the code of life, and just how it works to produce everything from bacteria to humans. 

So there you have it, that's my workplace and my job. DNA, RNA, lots of methods and a cool piece of technology that has turned genetics on its head and allowed geneticists to think big and detailed. 

Cobwebs and Tumbleweed....and how negativity can be detrimental to awesome science

My poor little blog. Sitting neglected for almost 11 months. Nearly a year. Honestly, I can't say where that time went. It just….went.

A year in terms of the solar system is less than a blink of an eye. But to a human, the time it takes for our humble little world to make one elliptical trip around the sun, well, much can happen in that same amount of time to one little being with an average lifespan of 75 years.

So what's been happening to prevent me from revisiting my little piece of the internet? The answer is simple: Life.

The last year has been, for lack of a better world, insane.  I departed from much that I was familiar with, both in the personal and professional world. Much of 2013 was marred by that dreaded feeling that permeates us from time to time - feeling lost, feeling worthless, and falling into the black hole of being overwhelmed. My work took on a whole new dimension including many more duties and while it meant immense personal growth and generally doing kick-ass science, it also resulted in me feeling really overwhelmed. On a more personal level, well, I faced the biggest upheaval of my adult life, and realised my relationship just wasn't right.  While hard to walk away, and the following months trying to rebuild myself, it was necessary. Add the fact the PhD writeup was dragging on and on, and I really had lost my motivation.

    Science is still awesome. Thanks Jesse for the reminder. 

And for this reason, I guess blogging about all things science, and  as well as sharing the things I find interesting about the universe fell by the wayside. But there's a lesson in all of this, because let's face it, there always is. 

 We all have bad days, we all have bad weeks, we all have bad months. And sometimes when you're finding life challenging, instead of supporting you those closest to you will turn around and make you feel like your ideas, your contribution, your blood, sweat and tears is not good enough.  It felt like this is all that happened last year. Have something bad happen, dig yourself out, have someone or something pull you right back down. Rinse and repeat.

And I let this get to me in a big way. I let it affect me to the point that my entire outlook changed and not for the pbetter. But the bigger realisation I had and the thing that brought me back from quitting due feeling sheer frustration and hoplessness is that people don't set out to make  you feel worthless  because you're actually bad at your work  or your ideas are bad.

What I've learnt from all of this is that much negativity from others stems in fact, from their insecurities.  Criticism is a necessary part of life. Science is an incredibly personal thing, so harsh critiscim can be hard to swallow. But criticism is very welcome in my world. However, criticism needs to be useful and not simple degrading, it must be constructive, it must be justified and it should be explained.  Deeming something unworthy because you don't like it, because you don't understand it, because you need to feel power by demeaning someone and to feed your own ego, these are the very things that are toxic to science. Science is based on evidence, and continuous evolution - of ideas, skills and knowledge. 

ANYBODY can say someone else is bad at something. 

The true test of whether they know what they are talking about and thus worth paying attention to comes next. If someone saying the work is invalid or poor, and can back this up with direction, with guidelines on how to improve, or how they can do better than you, then they are worth listening to. If not, then they're not worth paying attention or thought to. I've found it's that simple. This conclusion has helped me get back to where I need to be, and I can effectively screen out the negativity and stop letting it get to me and having an effect on my life. 

Anybody asking questions, pitching ideas or posing solutions and fostering discussion should be encouraged, not told they are unworthy. Curiosity and a desire to know more is a wonderful thing and frankly, there's not enough of it in the world. Shooting someone's ideas down for the sake of it forces them to become quiet and to withdraw.This is absolutely detrimental to scientific advancement. It kills the motivation of new students,and breeds contempt in more established researchers. Essentially, pure negativity creates loathing, it mars the joy of discovery, it kills collaboration, and most worryingly it also passes to the next generation, resulting in a new group of researchers who think the best way is to cut others down. We are all running on incredibly finite resources, we all should cut the crap and foster good ideas, collaboration and creativity, regardless of whether it's coming from a PhD student or a Federation Fellow. 

So, the moral of the story from the last 12 months: put up or shut up. If you are going to say someone's work is invalid, or they can't write, or they are crappy at their job, then you damn better be able to explain why or point them in the direction of tools to help them improve.  Otherwise you're having a negative effect on the scientific process, and you're the one not worthy of being part of the scientific community.